Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • EdgeR Normalization Question

    I am looking to do TMM normalization in an experiment where you have to do pairwise comparisons between 20+ samples in replicates of three (A1, A2, A3 vs B1, B2, B3; A1, A2, A3 vs C1, C2, C3; B1, B2, B3 vs C1,C2, C3 and so on).
    I was thinking that I should normalize all the samples together and then do pairwise comparisons.
    I was wondering how I can get EdgeR to give me the TMM normalized values in a csv file.
    Thanks!

  • #2
    There's actually no such thing as TMM normalized values. Normalization in edgeR is something that affects the fitted models rather than the data values. As the edgeR User's Guide says:

    "There are methods implemented in edgeR to normalize the counts for compositional bias in sequenced libraries and for diff erences between libraries in sequencing depth. These adjustments are off sets in the models used for testing DE and do not transform the counts in any way."

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Quality Control Essentials for Next-Generation Sequencing Workflows
      by seqadmin




      Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

      Nucleic Acid Quality Control
      Preparing for NGS starts with isolating the...
      02-10-2025, 01:58 PM
    • seqadmin
      An Introduction to the Technologies Transforming Precision Medicine
      by seqadmin


      In recent years, precision medicine has become a major focus for researchers and healthcare professionals. This approach offers personalized treatment and wellness plans by utilizing insights from each person's unique biology and lifestyle to deliver more effective care. Its advancement relies on innovative technologies that enable a deeper understanding of individual variability. In a joint documentary with our colleagues at Biocompare, we examined the foundational principles of precision...
      01-27-2025, 07:46 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 02-07-2025, 09:30 AM
    0 responses
    65 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-05-2025, 10:34 AM
    0 responses
    101 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 02-03-2025, 09:07 AM
    0 responses
    81 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 01-31-2025, 08:31 AM
    0 responses
    45 views
    0 likes
    Last Post seqadmin  
    Working...
    X